We have generated 145 ES cell lines thus far, in each of which one of a total of 145 different TFs can be overexpressed in a tetracycline-inducible manner. We have been characterizing these ES cell lines as follows: (i) subcellular localization of Flag-tagged transcription factors by immunohistochemistry;(ii) induction levels of the manipulated transcription factors by quantitative RT-PCR, (iii) DNA microarray-based expression profiling before and after the induction of transcription factors;(iv) western blotting, and (v) karyotyping. Together, these results indicate that we have generated reliable TF-manipulable ES cell lines. We have carried out detailed analyses of the first 50 ES cell lines and found that among the 50 TFs, Cdx2 provoked the most extensive transcriptome perturbation in ES cells, followed by Esx1, Sox9, Tcf3, Klf4, and Gata3. ChIP-Seq revealed that CDX2 binds to promoters of up-regulated target genes. By contrast, genes down-regulated by CDX2 did not show CDX2 binding, but were enriched with binding sites for POU5F1, SOX2, and NANOG. Genes with binding sites for these core TFs were also down-regulated by the induction of at least 15 other TFs, suggesting a common initial step for ES cell differentiation mediated by interference with the binding of core TFs to their target genes. We have recently completed the expression profiling of the remaining 95 ES cell lines and are currently analyzing the data. These ES cell lines provide a fundamental resource to study biological networks in ES cells and mice.